Variant report

Variant	rs2038041
Chromosome Location	chr1:171535573-171535574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171528756..171533659-chr1:171534422..171537081,4	MCF-7	breast:
2	chr1:171533246..171538102-chr1:171538740..171543133,5	K562	blood:
3	chr1:171535433..171538100-chr1:171538740..171541448,2	K562	blood:
4	chr1:171528043..171532235-chr1:171534961..171538235,5	K562	blood:
5	chr1:171527947..171533279-chr1:171534961..171539574,5	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10913119	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10913149	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10913157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10913197	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs10913285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10913292	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12080096	1.00[YRI][hapmap]
rs12564279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12567152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2038040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2179882	1.00[ASW][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs2294291	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3204333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57562814	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60014783	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6669168	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6676140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6681173	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6702038	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72717832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72717839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717840	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717853	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72717854	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7517178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7521480	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7522026	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv465639	chr1:171459507-171545051	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv548190	chr1:171459507-171545051	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171482200-171541800	Strong transcription	Primary B cells from peripheral blood	blood
2	chr1:171521600-171563800	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr1:171521800-171562800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:171522600-171564000	Strong transcription	Duodenum Mucosa	Duodenum
5	chr1:171522800-171564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:171522800-171564200	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr1:171522800-171564400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:171524200-171537800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:171524200-171537800	Strong transcription	Brain Anterior Caudate	brain
10	chr1:171524200-171538200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:171524200-171549600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:171524200-171562800	Strong transcription	Liver	Liver
13	chr1:171524200-171564400	Strong transcription	Adipose Nuclei	Adipose
14	chr1:171524400-171537600	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr1:171524400-171538200	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:171524400-171538400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:171524400-171541000	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:171524400-171549000	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:171524400-171549000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:171524400-171553000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:171524400-171558200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:171524400-171563600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:171524400-171564400	Strong transcription	Fetal Thymus	thymus
24	chr1:171524400-171564600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:171524400-171566400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:171524600-171537200	Strong transcription	Brain Hippocampus Middle	brain
27	chr1:171524600-171558600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:171524800-171537600	Strong transcription	Primary T cells from cord blood	blood
29	chr1:171525200-171555200	Strong transcription	Primary B cells from cord blood	blood
30	chr1:171525200-171564000	Strong transcription	HUVEC	blood vessel
31	chr1:171525400-171544400	Weak transcription	Stomach Mucosa	stomach
32	chr1:171525400-171563600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr1:171525600-171536600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:171525600-171538200	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr1:171525600-171549600	Strong transcription	NHDF-Ad	bronchial
36	chr1:171525600-171562200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:171525600-171562800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:171525600-171563800	Strong transcription	HSMM	muscle
39	chr1:171525800-171541000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:171525800-171552000	Strong transcription	Hela-S3	cervix
41	chr1:171525800-171564400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:171526200-171561800	Strong transcription	K562	blood
43	chr1:171526400-171538600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:171526800-171537400	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr1:171526800-171562800	Strong transcription	Dnd41	blood
46	chr1:171527200-171560600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:171527200-171562800	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:171528200-171563800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:171528400-171540000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:171528400-171545800	Weak transcription	Pancreas	Pancrea

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